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Mass extinctions are major influences on both the phylogenetic structure of the modern biota and our ability to reconstruct broad-based patterns of evolutionary history. The most recent mass extinction is also the most famous—that which implicates a bolide impact in defining the Cretaceous/Palaeogene boundary (K/Pg). Although the biotic effects of this event receive intensive scrutiny, certain ecologically important and diverse groups remain woefully understudied. One such group is the freshwater ray-finned fishes (Actinopterygii). These fish represent 25% of modern vertebrate diversity, yet the isolated and fragmentary nature of their K/Pg fossil record limits our understanding of their diversity dynamics across this event. Here, we address this problem using diversification analysis of molecular-based phylogenies alongside a morphotype analysis of fossils recovered from a unique site in the Denver Basin of western North America that provides unprecedented K/Pg resolution. Our results reveal previously unrecognized signals of post-K/Pg diversification in freshwater clades and suggest that the change was driven by localized and sporadic patterns of extinction. Supported inferences regarding the effects of the K/Pg event on freshwater fish also inform our expectations of how freshwater faunas might recover from the current biodiversity crisis.